Bacterial
whole-genome analysis
2024-02-08
Epidemiology
From Weisberg et al. 2021
Genome assemblies through time
From Koonin et al. 2021
Most frequent sequencing technologies
The current best way?
From Wick et al. 2023
The current best way? (cont.)
From Wick et al. 2023
Sequencing adapters - recap
After library prep, each DNA fragment is flanked by several types of short sequences that together make up the “adapters”:
Paired-end vs. single-end sequencing
In Illumina sequencing, DNA fragments can be sequenced from both ends as shown below — this is called “paired-end” (PE) sequencing:
When sequencing is instead single-end (SE), no reverse read is produced:
Paired-end sequencing
Paired-end sequencing is a way to effectively increase the read length.
The total size of the biological DNA fragment (without adapters) is often called the insert size:
Insert size variation
Insert size varies based on the library prep protocol aims, and because of variation due to limited precision in size selection. In some cases, the insert size can be:
- Shorter than the combined read length, leading to overlapping reads:
- Shorter than the single read length, leading to “adapter read-through” (i.e., the ends of the resulting reads will consist of adapter sequence, which should be removed):
Illumina error profile
Illumina error profile (cont.)
The different templates within a cluster get out of sync because occasionally:
They miss a base incorporation
They incorporate two bases at once
- Base incorporation may also terminate before the end of the template is reached
This error profile is why, for Illumina:
- There are hard limits on read lengths
- Base quality scores typically decrease along the read
Our pathogen
Pseudomonas syringae causes disease in a wide range of host plants, from Solanaceae and Leguminosae plants to citrus and stone fruit trees.
Pseudomonas syringae pv. syringae (Pss) is an emerging phytopathogen that causes Pseudomonas leaf spot (PLS) disease in pepper plants (Capsicum annuum var. annuum).
Copper-based antimicrobials are used as chemical control methods for Pss in peppers. This has resulted in the emergence of copper-resistant strains of Pss.
Variable genome vs. disease severity
Pangenomes
From Koonin et al. 2021